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Your output shows you should you should be ready to work with freesurfer version 6.0 which is an older release from ~2017.  So people there may have used version 6 for quite some time.   If there was something missing on the system that freesurfer 6 needed to run, it’s probably been remedied by now.  If you are just starting out with freesurfer then I would not be too concerned with using version 6.

Just keep in mind the current release is version 7.2.0 from this year (2021).  Browsing the 7.X release notes (at the top of the page) and comparing then with the 6.0 release notes (at the bottom of the page) can help you decide if version 7 offers improvements depending upon what you need to do - see  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes.  For ongoing work it’s recommended to stick with the version of freesurfer you started with  -  see the “Important Note” on this page, MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall.

- R.
On Sep 23, 2021, at 18:25, Banik, Rana <rana.banik@vanderbilt.edu> wrote:

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banikr2@banikr:~$ bash
banikr2@banikr:~$ export FREESURFER_HOME=/usr/local/freesurfer
banikr2@banikr:~$ source SFREESURFER_HOME/SetUpFreeSurfer.sh

bash: SFREESURFER_HOME/SetUpFreeSurfer.sh: No such file or directory

Instead, I changed the command as: 
banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.sh

gives the following: 
banikr2@banikr:~$ source /usr/local/freesurfer/SetUpFreeSurfer.sh
-------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer
FSFAST_HOME       /usr/local/freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/subjects
MNI_DIR           /usr/local/freesurfer/mni
FSL_DIR           /usr/local/fsl

How do I check the installation is done properly? 
FYI, I have used mri_convert from python script.

Rana Banik

From: fsbuild <fsbuild@contbay.com>
Sent: Thursday, September 23, 2021 4:11 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Banik, Rana <rana.banik@vanderbilt.edu>
Subject: Re: [Freesurfer] freesurfer running error at start
 
OK, then try setting FREESURFER_HOME and setting the environment in a terminal window with the commands,

$ bash
$ export FREESURFER_HOME=/usr/local/freesurfer
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

Then you should see what the output reports for the freesurfer version.

- R.

On Sep 23, 2021, at 15:30, Banik, Rana <rana.banik@vanderbilt.edu> wrote:

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Hello, 

There is no directory called /7.2.0 rather the directory i am finding the files is: 
<pre><font color="#8AE234"><b>banikr2@banikr</b></font>:<font color="#729FCF"><b>/usr/local/freesurfer</b></font>$ pwd
/usr/local/freesurfer
</pre>

Trying the same in the /freesurfer folder

Rana Banik

From: fsbuild <fsbuild@contbay.com>
Sent: Wednesday, September 22, 2021 7:11 PM
To: freesurfer@nmr..mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Cc: Banik, Rana <rana.banik@vanderbilt.edu>
Subject: Re: [Freesurfer] freesurfer running error at start
 
Hello Rana,

Running that script (or any other freesurfer commands/binaries) assumes you’ve setup the freesurfer environment by,

1) setting FREESURFER_HOME in your shell to point to the top of the freesurfer tree
2) source’ing a shell init file to set PATH and other environment variables in order to run freesurfer commands

There is info on the wiki about this for linux,
- and the Mac,

Just find the absolute path to the top of the freesurfer tree.  For the latest 7.2.0 release installed by the package installers the version number is already in the absolute pathname to the top of the freesurfer tree.  On linux that path would be /usr/local/freesurfer/7.2.0 and on the Mac that path would be /Applications/freesurfer/7.2.0

For that linux path using bash you would do,
$ bash
$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0
$ source $FREESURFER_HOME/SetUpFreeSurfer.sh

When you run the source command to read the SetUpFreeSurfer script for the shell you are using, the version of freesurfer will get printed out automatically for you.

Using the 7.2.0 linux release you would see the string between the dashes no matter what the absolute path is to FREESURFER_HOME on your system.

tmp$ export FREESURFER_HOME=/usr/local/freesurfer/7.2.0
tmp$ source $FREESURFER_HOME/SetUpFreeSurfer.sh
-------- freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /usr/local/freesurfer/7.2.0
FSFAST_HOME       /usr/local/freesurfer/7.2.0/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /usr/local/freesurfer/7.2.0/subjects
MNI_DIR           /usr/local/freesurfer/7.2.0/mni
FSL_DIR           /usr/pubsw/packages/fsl/current

… now run any freesurfer commands …

- R

On Sep 22, 2021, at 18:04, Banik, Rana <rana.banik@vanderbilt.edu> wrote:

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Running freesurfer from terminal with the following error: 

banikr2@banikr:~/freesurfer/bin$ ./freesurfer 

FreeSurfer is a set of tools for the analysis and visualization
of structural and functional brain imaging data. FreeSurfer
also refers to the structural imaging stream within the
FreeSurfer suite.

Users should consult the online documentation available at:

  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://surfer.nmr.mgh.harvard.edu

Alternatively, the 'recon-all' command help-text provides
adequate information to begin processing subject data, such
as the sample subject 'bert' found in the 'freesurfer/subjects'
directory.  Type 'recon-all --help' to view this help-text.

Direct comments and questions to:

  freesurfer@nmr.mgh.harvard.edu

You are running this version of FreeSurfer:

cat: /build-stamp.txt: No such file or directory

Any idea what went wrong or how to fix it? 

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